Alignments for a candidate for agx1 in Azospirillum brasilense Sp245

GapMind for Amino acid biosynthesis

Alignments for a candidate for agx1 in Azospirillum brasilense Sp245

Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate AZOBR_RS27880 AZOBR_RS27880 4-aminobutyrate aminotransferase

Query= SwissProt::Q94AL9
         (477 letters)



>FitnessBrowser__azobra:AZOBR_RS27880
          Length = 438

 Score =  293 bits (749), Expect = 1e-83
 Identities = 167/417 (40%), Positives = 245/417 (58%), Gaps = 12/417 (2%)

Query: 61  ILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVE 120
           ++++R+  L P+    Y  P+++V G+   L+D  G RYLDA+  +A V  GH  P+VVE
Sbjct: 22  LIARRERLLGPAYRLFYADPIHVVRGEGSSLYDAEGNRYLDAYNNVASV--GHSRPEVVE 79

Query: 121 PVINQIKRLQHPTVLYLNHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYT 180
            +  Q   L   T  YL   I DF+EA  ++ P +L  +  T +G+EAN+LAL +A+++T
Sbjct: 80  AMARQAAVLNTHT-RYLTDGILDFAEAFLAEFPAELSHLMLTCTGSEANDLALRVARVHT 138

Query: 181 GCQDIVAVRNGYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKD 240
           G   +V   N YHG  +A +     S+     + + V     PD YR      G  +A+ 
Sbjct: 139 GGTGVVIAHNAYHGVTSA-LAEMSPSLGAAVKLGDHVRVVPAPDGYRMPEAEVGAAFARS 197

Query: 241 LQ----DLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQS 296
           ++    DL + G T   A  + + I    G+     G+L+ A + ++KAGG+FIADEVQ 
Sbjct: 198 VEEAIADLREKGITP--AALLVDTIFSSSGVFTDPAGFLAPAVEVMRKAGGVFIADEVQP 255

Query: 297 GFARTG-NFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTR-RSYFNTFGGN 354
           GF R G + WGF  H +VPDIVT+ K +GNG P+   V  PE+     + + YFNTFGGN
Sbjct: 256 GFGRLGTHMWGFARHGLVPDIVTVGKPMGNGHPVAGAVFRPEVIEAFGKSQRYFNTFGGN 315

Query: 355 SVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVS 414
            VS    LAVL VI++++LQENA  VG+ + + L  L  KHE+IGDVRG GL +GVE+V 
Sbjct: 316 PVSCAVALAVLRVIKEDRLQENALTVGTEMIDGLRALAAKHELIGDVRGSGLFIGVEMVR 375

Query: 415 DRKLKTPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAMD 471
           DRKLKTPA+ ET  +++ M++  VLI   G  G++ +I PPL F+ +DA   +  +D
Sbjct: 376 DRKLKTPASEETARVVNGMRQRRVLISATGQEGHILKIRPPLVFSSEDAKLFLATLD 432


Lambda     K      H
   0.320    0.136    0.403 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 530
Number of extensions: 31
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 477
Length of database: 438
Length adjustment: 33
Effective length of query: 444
Effective length of database: 405
Effective search space:   179820
Effective search space used:   179820
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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Protein sequences (fasta format)
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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis